Status
Public on Jun 23, 2024
Title
Dnmt3b_ff,rep2
Sample type
SRA
Source name
Dnmt3b_f/f
Characteristics
cell line: Dnmt3b_f/f
cell type: mESCs
genotype: WT
Extracted molecule
genomic DNA
Extraction protocol
Genomic DNA was extracted by phenol chloroform dna extraction
Preparation of genomic DNA. The cells were suspended in a buffer comprising 20 mM Tris-HCl, pH 8.0, 0.4 M NaCl, 10 mM EDTA, 0.5% SDS, and 0.1 mg/ml RNase A, and then incubated at 37°C for 1 h. Proteinese K was added to the sample at a concentration of 1 mg/ml, and then incubated at 56°C for overnight. The sample was treated with phenol/chloroform followed by ethanol precipitation. The genomic DNA was dissolved in TE buffer. Preparation of the library. The genomic DNA (1 μg) was sheared by sonication to 100–500 bp using a Covaris S220 and purified by AMPure XP beads (Agencourt Bioscience Corp.). Then, genomic DNA libraries were constructed by KAPA Hyper Prep Kit (Kapa Biosystems) and xGen Stubby Adapter and UDI Primers Pairs kit (Integrated DNA technologies) according to manufacturer instructions. After adapter ligation, the DNA was treated with sodium bisulfite using EZ DNA Methylation GOLD kit (Zymo Research) following the manufacturer's instructions. Enrichment for adapter-ligated DNA was carried out through 17 PCR cycles using KOD One PCR Master mix (Toyobo). The concentration of the WGBS library was quantified by KAPA Library quantification kit (Kapa Biosystems). Paired-end DNA sequencing (2 ×ばつ 150 bp) was then performed using the Illumina NovaSeq X plus (Illumina). We performed two technical replicates for WGBS. Each library was sequenced with 21–24 M read pairs.
MethylC-seq
Library strategy
OTHER
Library source
genomic
Library selection
other
Instrument model
Illumina NovaSeq X Plus
Data processing
Adaptor sequences and low quality bases in reads were trimmed using Trim Galore version 0.3.7
The trimmed reads were mapped to the mouse GRCm38 genome assembly using Bismark v0.24.1 with paired-end and non-directional mapping parameters
The methylation level of each CpG site was calculated as follows: number of methylated reads/number of total reads.
Assembly: mm10
Supplementary files format and content: txt
Submission date
Jun 18, 2024
Last update date
Jun 23, 2024
Contact name
Kei Fukuda
Organization name
RIKEN
Lab
Cellular memory
Street address
2-1 Hrosawa, Wakoshi
City
Saitama
State/province
Japan
ZIP/Postal code
351-0198
Country
Japan
Series (1)
GSE270227
The C-terminal 4CXXC-type zinc finger domain of CDCA7 recognizes hemimethylated DNA and modulates activities of chromatin remodeling enzyme HELLS
Relations
Supplementary file
Size
Download
File type/resource
GSM8337517_Dnmt3b_ff_2.meth.gz
60.4 Mb
(ftp) (http)
METH
Raw data are available in SRA